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Yorodumi- PDB-8dio: Crystal structure of LARP1-DM15 from Danio rerio bound to m7GpppC -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dio | |||||||||
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Title | Crystal structure of LARP1-DM15 from Danio rerio bound to m7GpppC | |||||||||
Components | La ribonucleoprotein 1, translational regulator | |||||||||
Keywords | RNA BINDING PROTEIN / LARP1 / DM15 | |||||||||
Function / homology | Chem-91P / 2-amino-7-methyl-1,7-dihydro-6H-purin-6-one / : Function and homology information | |||||||||
Biological species | Danio rerio (zebrafish) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Nguyen, E. / Berman, A.J. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published Title: Comparative analysis of the LARP1 C-terminal DM15 region through Coelomate evolution Authors: Nguyen, E. / Berman, A.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dio.cif.gz | 231 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dio.ent.gz | 157.5 KB | Display | PDB format |
PDBx/mmJSON format | 8dio.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dio_validation.pdf.gz | 891.2 KB | Display | wwPDB validaton report |
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Full document | 8dio_full_validation.pdf.gz | 899.3 KB | Display | |
Data in XML | 8dio_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 8dio_validation.cif.gz | 20.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/di/8dio ftp://data.pdbj.org/pub/pdb/validation_reports/di/8dio | HTTPS FTP |
-Related structure data
Related structure data | 8dhuC 5v87S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18843.410 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: larp1 / Production host: Escherichia coli (E. coli) / References: UniProt: F1R0U5 #2: Chemical | ChemComp-91P / [[( | #3: Chemical | ChemComp-MY6 / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.49 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 50 mM HEPES, pH 7, 0 or 100 mM NaCl, 2 mM DTT |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 16, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→47.18 Å / Num. obs: 13814 / % possible obs: 91.78 % / Redundancy: 2 % / Biso Wilson estimate: 19.43 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.0145 / Net I/σ(I): 28.43 |
Reflection shell | Resolution: 2.3→2.382 Å / Redundancy: 2 % / Num. unique obs: 1391 / CC1/2: 0.998 / CC star: 1 / % possible all: 93.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5V87 Resolution: 2.3→47.18 Å / SU ML: 0.2395 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.8655 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.53 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→47.18 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -3.13743205247 Å / Origin y: 16.1561648962 Å / Origin z: -15.2470063745 Å
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Refinement TLS group | Selection details: all |